Current Research Projects

Although the laboratory methods for generating genetic sequence data have advanced remarkably in recent years, the computational methods used to analyze and glean understanding from this data have not advanced as dramatically. Genome sequencing relies on {\em sequencing platforms} that accept a collection of DNA samples and produce a set of strings representing the sequence of nucleotides in a sample, which are known as {\em reads}. High-throughput sequencing platforms produce billions of short sequence reads per run, permitting assembly algorithms to exploit the redundancy in the data in order to produce longer sequences corresponding to the genome.

The rapid increase in the production of these reads and the development of new technology has prompted many new computational problems that have not been sufficiently addressed. My research lab resolves these computational problems by developing holistic, multi-omics tools that answer key biological questions. In particular, we work on the following problems: (1) development of optical mapping data analysis methods, (2) creation of automated misassembly detection programs, and (3) advancement of computational analysis of antimicrobial resistance data.